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Collections
Gather and organize Capsules, Pipelines, Apps, and Data by project or scientific area of interest to make them more visible, accessible, and usable by others.
Key capabilities
Organize your team's computational assets
Owners of release versions of Compute Capsules, Pipelines, Apps, and Data can add them to Collections within your organization. Admin-defined Collections trees enforce structure.
Find everything you're looking for in one place
Surfacing computational work to make it more visible for the wider organization can be difficult. Collections make it straightforward to organize everything and see what’s available.
How Collections work with the rest of the Code Ocean platform
Organize Compute Capsules
Organize Pipelines
Organize Data
Frequently asked questions
Collections
What can be added to a Collection?
You can add all four of the main computational assets in Code Ocean: Compute Capsules, Pipelines, no-code Apps, and Data.
Who can add assets to a Collection?
The owner(s) of an asset can add or remove it from a Collection.
Are all assets in Collections visible to all users?
No. Every asset has its own access permissions. Users will only see what they have permission to see in a Collection.
How do we set up the Collections folder structure?
Admins determine the Collections folder structure for the organization.
Built for Computational Science
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Data analysis
Data analysis
Use ready-made template Compute Capsules to analyze your data, develop your data analysis workflow in your preferred language and IDE using any open-source software, and take advantage of built-in containerization to guarantee reproducibility.
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Data management
Data management
Manage your organization's data and control who has access to it. Built specifically to meet all FAIR principles, data management in Code Ocean uses custom metadata and controlled vocabularies to ensure consistency and improve searchability.
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Bioinformatics pipelines
Bioinformatics pipelines
Build, configure and monitor bioinformatics pipelines from scratch using a visual builder for easy set-up. Or, import from nf-core in one click for instant access to a curated set of best practice analysis pipelines. Runs on AWS Batch out-of-the-box, so your pipelines scale automatically. No setup needed.
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ML models
ML model development
Code Ocean is uniquely suited for Artificial Intelligence, Machine Learning, Deep Learning, and Generative AI. Install GPU-ready environments and provision GPU resources in a few clicks. Integration with MLFlow allows you to develop models, track parameters, manage models from development to production, while enjoying out-of-the-box reproducibility and lineage.
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Multiomics
Multiomics
Analyze and work with large multimodal datasets efficiently using scalable compute and storage resources, cached packages for R and Python, preloaded multiomics analysis software that works out of the box and full lineage and reproducibility.
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Imaging
Imaging
Process images using a variety of tools: from dedicated desktop applications to custom-written deep learning pipelines, from a few individual files to petabyte-sized datasets. No DevOps required, always with lineage.
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Cloud management
Cloud management
Code Ocean makes it easy to manage data and provision compute: CPUs, GPUs, and RAM. Assign flex machines and dedicated machines to manage what is available to your users. Spot instances, idleness detection, and automated shutdown help reduce cloud costs.
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Data/model provenance
Data/model provenance
Keep track of all data and results with automated result provenance and lineage graph generation. Assess reproducibility with a visual representation of every Capsule, Pipeline, and Data asset involved in a computation.
Data analysis
Use ready-made template Compute Capsules to analyze your data, develop your data analysis workflow in your preferred language and IDE using any open-source software, and take advantage of built-in containerization to guarantee reproducibility.
Data management
Manage your organization's data and control who has access to it. Built specifically to meet all FAIR principles, data management in Code Ocean uses custom metadata and controlled vocabularies to ensure consistency and improve searchability.
Bioinformatics pipelines
Build, configure and monitor bioinformatics pipelines from scratch using a visual builder for easy set-up. Or, import from nf-core in one click for instant access to a curated set of best practice analysis pipelines. Runs on AWS Batch out-of-the-box, so your pipelines scale automatically. No setup needed.
ML model development
Code Ocean is uniquely suited for Artificial Intelligence, Machine Learning, Deep Learning, and Generative AI. Install GPU-ready environments and provision GPU resources in a few clicks. Integration with MLFlow allows you to develop models, track parameters, manage models from development to production, while enjoying out-of-the-box reproducibility and lineage.
Multiomics
Analyze and work with large multimodal datasets efficiently using scalable compute and storage resources, cached packages for R and Python, preloaded multiomics analysis software that works out of the box and full lineage and reproducibility.
Imaging
Process images using a variety of tools: from dedicated desktop applications to custom-written deep learning pipelines, from a few individual files to petabyte-sized datasets. No DevOps required, always with lineage.
Cloud management
Code Ocean makes it easy to manage data and provision compute: CPUs, GPUs, and RAM. Assign flex machines and dedicated machines to manage what is available to your users. Spot instances, idleness detection, and automated shutdown help reduce cloud costs.
Data/model provenance
Keep track of all data and results with automated result provenance and lineage graph generation. Assess reproducibility with a visual representation of every Capsule, Pipeline, and Data asset involved in a computation.
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